diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
index ab1810dd4e548f66bcafe189f74b559d73a908fa..4337be731d283e5c341bccb14e0a93a00b2811fd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ImproperAnnotations.java
@@ -19,9 +19,9 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
 public class ImproperAnnotations implements ProblematicAnnotation {
 
 	/**
-	 * Object improperly annotated.
+	 * {@link BioEntity} improperly annotated.
 	 */
-	private BioEntity	 object;
+	private BioEntity				 bioEntity;
 
 	/**
 	 * Wrong miriam data.
@@ -29,39 +29,39 @@ public class ImproperAnnotations implements ProblematicAnnotation {
 	private List<MiriamData> wrongAnnotations	= new ArrayList<>();
 
 	/**
-	 * Constructor that initializes the data with {@link #object bioEntity}
-	 * and list of improper {@link MiriamData}.
+	 * Constructor that initializes the data with {@link #bioEntity bioEntity} and
+	 * list of improper {@link MiriamData}.
 	 * 
 	 * @param list
 	 *          list of improper {@link MiriamData}
-	 * @param object
-	 *          annotated object
+	 * @param bioEntity
+	 *          bioentity
 	 */
-	public ImproperAnnotations(BioEntity object, List<MiriamData> list) {
+	public ImproperAnnotations(BioEntity bioEntity, List<MiriamData> list) {
 		if (list.size() == 0) {
 			throw new InvalidArgumentException("List of improper annotations cannot be null");
 		}
-		this.object = object;
+		this.bioEntity = bioEntity;
 		wrongAnnotations.addAll(list);
 	}
 
 	/**
-	 * Constructor that initializes the data with {@link #object annotated object}
+	 * Constructor that initializes the data with {@link #bioEntity bio entity}
 	 * and improper {@link MiriamData}.
 	 * 
 	 * @param miriamData
 	 *          invalid {@link MiriamData}
-	 * @param object
+	 * @param bioEntity
 	 *          annotated object
 	 */
-	public ImproperAnnotations(BioEntity object, MiriamData miriamData) {
-		this.object = object;
+	public ImproperAnnotations(BioEntity bioEntity, MiriamData miriamData) {
+		this.bioEntity = bioEntity;
 		wrongAnnotations.add(miriamData);
 	}
 
 	@Override
 	public String getMessage() {
-		StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(object));
+		StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
 		result.append("contains invalid annotations: ");
 		for (MiriamData miriamData : wrongAnnotations) {
 			result.append(miriamData.getDataType().getCommonName() + "(" + miriamData.getResource() + "), ");
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
index 64aa9a4bc144eb9929a04c835a26ed11576d88a4..d981d5a1ba502f44a0d1a137780f5633cc275dbd 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingAnnotation.java
@@ -13,24 +13,23 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
 public class MissingAnnotation implements ProblematicAnnotation {
 
 	/**
-	 * Object improperly annotated.
+	 * BioEntity improperly annotated.
 	 */
-	private BioEntity object;
+	private BioEntity bioEntity;
 
 	/**
-	 * Constructor that initializes the data with {@link #object annotated object}
-	 * .
+	 * Constructor that initializes the data with {@link #bioEntity bioEntity} .
 	 * 
-	 * @param object
-	 *          annotated object that miss annotation
+	 * @param bioEntity
+	 *          bioEntity that misses annotation
 	 */
-	public MissingAnnotation(BioEntity object) {
-		this.object = object;
+	public MissingAnnotation(BioEntity bioEntity) {
+		this.bioEntity = bioEntity;
 	}
 
 	@Override
 	public String getMessage() {
-		return new ElementUtils().getElementTag(object) + "misses annotations.";
+		return new ElementUtils().getElementTag(bioEntity) + "misses annotations.";
 	}
 
 	@Override
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
index c6a40a2e92f5e24e502ac300aaefd66d7d0acbe6..c2ba975f0ed8d4665764239e5ddbb71ac1d4e9dc 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/MissingRequiredAnnotations.java
@@ -12,7 +12,7 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
 
 /**
  * Defines problem with element annotation when there are some required
- * annotations,but none of them can be found in the element.
+ * annotations, but none of them can be found in the element.
  * 
  * @author Piotr Gawron
  *
@@ -20,9 +20,9 @@ import lcsb.mapviewer.modelutils.map.ElementUtils;
 public class MissingRequiredAnnotations implements ProblematicAnnotation {
 
 	/**
-	 * Object improperly annotated.
+	 * BioEntity improperly annotated.
 	 */
-	private BioEntity	 object;
+	private BioEntity				 bioEntity;
 
 	/**
 	 * Required miriam type.
@@ -30,25 +30,25 @@ public class MissingRequiredAnnotations implements ProblematicAnnotation {
 	private List<MiriamType> requiredMiriamType	= new ArrayList<>();
 
 	/**
-	 * Constructor that initializes the data with {@link #object annotated object}
-	 * and list of improper {@link MiriamData}.
+	 * Constructor that initializes the data with {@link #bioEntity bioEntity} and
+	 * list of improper {@link MiriamData}.
 	 * 
 	 * @param list
 	 *          list of missing but required {@link MiriamType}
-	 * @param object
-	 *          annotated object
+	 * @param bioEntity
+	 *          {@link BioEntity}
 	 */
-	public MissingRequiredAnnotations(BioEntity object, Collection<MiriamType> list) {
+	public MissingRequiredAnnotations(BioEntity bioEntity, Collection<MiriamType> list) {
 		if (list.size() == 0) {
 			throw new InvalidArgumentException("List of improper annotations cannot be null");
 		}
-		this.object = object;
+		this.bioEntity = bioEntity;
 		requiredMiriamType.addAll(list);
 	}
 
 	@Override
 	public String getMessage() {
-		StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(object));
+		StringBuilder result = new StringBuilder(new ElementUtils().getElementTag(bioEntity));
 		result.append("misses one of the following annotations: ");
 		for (MiriamType type : requiredMiriamType) {
 			result.append(type.getCommonName());
diff --git a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
index 9808ebd014b966acec5a64d4c7f9a14290e65fa0..fb21e1e31b1a74f5dfe67cd9121e222938112d03 100644
--- a/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
+++ b/annotation/src/main/java/lcsb/mapviewer/annotation/services/ModelAnnotator.java
@@ -428,8 +428,8 @@ public class ModelAnnotator {
 	}
 
 	/**
-	 * Checks if {@link BioEntity} is properly annotated and if not return
-	 * info about missing annotation.
+	 * Checks if {@link BioEntity} is properly annotated and if not return info
+	 * about missing annotation.
 	 * 
 	 * @param element
 	 *          object to be checked
@@ -604,7 +604,7 @@ public class ModelAnnotator {
 	 * miriam types } for {@link BioEntity} class type.
 	 * 
 	 * @return map with informations about required {@link MiriamType miriam types
-	 *         * } for {@link BioEntity} class type
+	 *         } for {@link BioEntity} class type
 	 */
 	@SuppressWarnings("unchecked")
 	public Map<Class<? extends BioEntity>, Set<MiriamType>> getDefaultRequiredClasses() {